Dion Hinchcliffe put together a great list of the best Web 2.0 applications released in 2005. Interestingly, only one of about 30 applications has been developed by a big corporation (Microsoft's Start.com) while the rest has been developed by start-ups - some of them tiny one- or two-person companies. As far as Web 2.0 is concerned, the greatest innovations still come from start-ups (although the GYM is close, as demonstrated with software like Google Earth and the new Yahoo! Mail).
So far, two from the list have been acquired by one of the big boys: Flickr and Del.icio.us. I'm sure that in a year from now, a couple of others from the list will have been snapped up. My best guesses are Writely and Netvibes.
Congrats to Sam (Writely), Tariq (Netvibes), Ian (Openomy), Jason (Writeboard and Ta-Da-List) and to everyone else who's working on the next generation of Internet software.
Last but not least some sites I'd suggest to add: